Mercurial > repos > matt-shirley > sra_tools
comparison sam_dump.xml @ 1:75d914fa5711 draft default tip
Moving repository to testtoolshed for now.
| author | matt-shirley |
|---|---|
| date | Tue, 27 Nov 2012 13:43:03 -0500 |
| parents | cdcc400dcafc |
| children |
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| 0:cdcc400dcafc | 1:75d914fa5711 |
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| 1 <tool id="sam_dump" name="Extract SAM" version="1.0.0"> | |
| 2 <description> format reads from NCBI SRA.</description> | |
| 3 <command>sam-dump $header $aligned $primary '$input' > $output</command> | |
| 4 <version_string>sam-dump --version</version_string> | |
| 5 <inputs> | |
| 6 <param format="sra" name="input" type="data" label="sra archive"/> | |
| 7 <param format="text" name="header" type="select" value=""> | |
| 8 <label>Output SAM header</label> | |
| 9 <option value="--header">Yes</option> | |
| 10 <option value="--no-header">No</option> | |
| 11 </param> | |
| 12 <param format="text" name="aligned" type="select" value=""> | |
| 13 <label>Output unaligned reads</label> | |
| 14 <option value="">No</option> | |
| 15 <option value="--unaligned">Yes</option> | |
| 16 </param> | |
| 17 <param format="text" name="primary" type="select" value=""> | |
| 18 <label>Output only primary aligments</label> | |
| 19 <option value="">No</option> | |
| 20 <option value="--primary">Yes</option> | |
| 21 </param> | |
| 22 </inputs> | |
| 23 <outputs> | |
| 24 <data format="sam" name="output"/> | |
| 25 </outputs> | |
| 26 <requirements> | |
| 27 <requirement type="binary">sam-dump</requirement> | |
| 28 </requirements> | |
| 29 <help> | |
| 30 This tool extracts SAM format reads from SRA archives using sam-dump. The sam-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. | |
| 31 Contact Matt Shirley at mdshw5@gmail.com for support and bug reports. | |
| 32 </help> | |
| 33 </tool> |